suppressPackageStartupMessages({
library(tidyverse)
})
# Detect the ".git" folder -- this will be in the project root directory
# Use this as the root directory to ensure proper sourcing of functions
# no matter where this is called from
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
analysis_dir <- file.path(root_dir, "analyses", "tmb-vaf-longitudinal")
results_dir <- file.path(analysis_dir, "results")
input_dir <- file.path(analysis_dir, "input")
files_dir <- file.path(root_dir, "analyses", "sample-distribution-analysis", "results")
# Input files for the paired longitudinal (PR) cohort
pbta_file <- file.path(files_dir, "pbta.tsv") # file from add-sample-distribution module
genomic_paired_file <- file.path(files_dir, "genomic_assays_matched_time_points.tsv")
tmb_vaf_file <- file.path(results_dir, "tmb_vaf_genomic.tsv")
palette_file <- file.path(root_dir, "figures", "palettes", "oncoprint_color_palette.tsv")
# Input files for the PBTA cohort
maf_file <- file.path(results_dir, "maf.tsv")
tmb_file <- file.path(input_dir, "snv-mutation-tmb-coding.tsv")
# File path to PR plot directory
PR_plots_dir <-
file.path(analysis_dir, "plots", "Alteration_type_barplots_PR")
if (!dir.exists(PR_plots_dir)) {
dir.create(PR_plots_dir)
}
# File path to kids_PR_plots directory
kids_PR_plots_dir <-
file.path(PR_plots_dir, "kids_PR_plots")
if (!dir.exists(kids_PR_plots_dir)) {
dir.create(kids_PR_plots_dir)
}
# File path to kids_molecular_subtype_PR_plots_dir directory
kids_molecular_subtype_PR_plots_dir <-
file.path(PR_plots_dir, "kids_molecular_subtype_PR_plots")
if (!dir.exists(kids_molecular_subtype_PR_plots_dir)) {
dir.create(kids_molecular_subtype_PR_plots_dir)
}
# File path to molecular_subtype_PR_plots directory
molecular_subtype_PR_plots_dir <-
file.path(PR_plots_dir, "molecular_subtype_PR_plots")
if (!dir.exists(molecular_subtype_PR_plots_dir)) {
dir.create(molecular_subtype_PR_plots_dir)
}
# File path to PBTA plot directory
PBTA_plots_dir <-
file.path(analysis_dir, "plots", "Alteration_type_barplots_PBTA")
if (!dir.exists(PBTA_plots_dir)) {
dir.create(PBTA_plots_dir)
}
# File path to molecular_subtype_PBTA_plots directory
molecular_subtype_PBTA_plots_dir <-
file.path(PBTA_plots_dir, "molecular_subtype_PBTA_plots")
if (!dir.exists(molecular_subtype_PBTA_plots_dir)) {
dir.create(molecular_subtype_PBTA_plots_dir)
}
source(paste0(root_dir, "/figures/scripts/theme.R"))
source(paste0(analysis_dir, "/util/function-create-barplot.R"))
# Vector to order timepoints
timepoints_order <- c("Diagnosis", "Progressive", "Recurrence", "Deceased", "Second Malignancy", "Unavailable")
# Vector to order Variant_Classification
variants_order <- c("Frame_Shift_Del", "Frame_Shift_Ins", "In_Frame_Del",
"In_Frame_Ins", "Missense_Mutation", "Nonsense_Mutation",
"Nonstop_Mutation", "Splice_Site", "Translation_Start_Site")
pbta_df <- readr::read_tsv(pbta_file, guess_max = 100000, show_col_types = FALSE) %>%
select(Kids_First_Participant_ID, Kids_First_Biospecimen_ID, cg_multiple, cg_id, cgGFAC, tumor_descriptor, molecular_subtype)
# This includes non synonymous mutations as described in the `01-preporcess-data.Rmd`
tmb_vaf_df <- readr::read_tsv(tmb_vaf_file, guess_max = 100000, show_col_types = FALSE) %>%
filter(!tmb >= 10) %>%
select(Kids_First_Biospecimen_ID, Variant_Classification, gene_protein, mutation_count, region_size, tmb, VAF)
genomic_paired_df <- readr::read_tsv(genomic_paired_file, guess_max = 100000, show_col_types = FALSE) %>%
left_join(pbta_df, by = c("Kids_First_Participant_ID")) %>%
left_join(tmb_vaf_df, by = c("Kids_First_Biospecimen_ID")) %>%
filter(!is.na(tmb))
no_samples_with_tmb <- print(length(unique(genomic_paired_df$Kids_First_Participant_ID)))
[1] 116
# Attention as some bs specimen might not have TMB.
# If that happens, we will end up with samples lacking timepoints.
# Let's identify these samples and remove them for now.
PR_df <- genomic_paired_df %>%
select(Kids_First_Participant_ID, tumor_descriptor) %>%
unique() %>%
arrange(Kids_First_Participant_ID, tumor_descriptor) %>%
group_by(Kids_First_Participant_ID) %>%
summarize(tumor_descriptor_sum = str_c(tumor_descriptor, collapse = ";")) %>%
filter(!tumor_descriptor_sum %in% c("Diagnosis", "Progressive", "Recurrence", "Second Malignancy", "Unavailable", "Deceased", "Progressive;Progressive")) %>%
left_join(genomic_paired_df, by = c("Kids_First_Participant_ID")) %>%
filter(!cg_id == "NA",
!tumor_descriptor == "Not Reported") %>%
mutate(match_id = paste(tumor_descriptor, Kids_First_Participant_ID, sep = "_"),
cg_id = str_replace(cg_id, c("/|-"), " "))
no_samples <- print(length(unique(PR_df$Kids_First_Participant_ID)))
[1] 107
# Let's count number of samples
PR_count_df <- PR_df %>%
group_by(tumor_descriptor, cg_id, molecular_subtype, Kids_First_Participant_ID, match_id, Variant_Classification) %>%
dplyr::count(cg_id) %>%
mutate(tumor_descriptor = factor(tumor_descriptor),
tumor_descriptor = fct_relevel(tumor_descriptor, timepoints_order),
Variant_Classification = factor(Variant_Classification),
Variant_Classification = fct_relevel(Variant_Classification, variants_order)) %>%
arrange(tumor_descriptor, Variant_Classification)
Warning: There were 945 warnings in `mutate()`.
The first warning was:
ℹ In argument: `tumor_descriptor = fct_relevel(tumor_descriptor, timepoints_order)`.
ℹ In group 1: `tumor_descriptor = "Deceased"`, `cg_id = "Adamantinomatous Craniopharyngioma"`, `molecular_subtype = "CRANIO, ADAM"`,
`Kids_First_Participant_ID = "PT_WYXTEG3E"`, `match_id = "Deceased_PT_WYXTEG3E"`, `Variant_Classification = "Frame_Shift_Del"`.
Caused by warning:
! 1 unknown level in `f`: Unavailable
ℹ Run ]8;;ide:run:dplyr::last_dplyr_warnings()dplyr::last_dplyr_warnings()]8;; to see the 944 remaining warnings.
tmb_df <- readr::read_tsv(tmb_file, guess_max = 100000, show_col_types = FALSE) %>%
dplyr::rename(Kids_First_Biospecimen_ID = Tumor_Sample_Barcode) # change name of the biospecimen to match the one from the histologies files
tmb_vaf_df <- readr::read_tsv(maf_file, guess_max = 100000, show_col_types = FALSE) %>%
left_join(tmb_df, by = c("Kids_First_Biospecimen_ID")) %>%
filter(!tmb >= 10,
!is.na(tmb))
PBTA_df <- pbta_df %>%
left_join(tmb_vaf_df, by = c("Kids_First_Biospecimen_ID")) %>%
filter(!cg_id == "NA",
!tumor_descriptor == "Not Reported") %>%
mutate(match_id = paste(tumor_descriptor, Kids_First_Participant_ID, sep = "_"),
cg_id = str_replace(cg_id, c("/|-"), " "))
no_samples <- print(length(unique(PBTA_df$Kids_First_Participant_ID)))
[1] 2153
# Let's count number of samples
PBTA_count_df <- PBTA_df %>%
group_by(tumor_descriptor, cg_id, molecular_subtype, Kids_First_Participant_ID, match_id, Variant_Classification) %>%
dplyr::count(cg_id) %>%
mutate(tumor_descriptor = factor(tumor_descriptor),
tumor_descriptor = fct_relevel(tumor_descriptor, timepoints_order),
Variant_Classification = factor(Variant_Classification),
Variant_Classification = fct_relevel(Variant_Classification, variants_order)) %>%
arrange(tumor_descriptor, Variant_Classification)
Warning: There were 8486 warnings in `mutate()`.
The first warning was:
ℹ In argument: `tumor_descriptor = fct_relevel(tumor_descriptor, timepoints_order)`.
ℹ In group 1: `tumor_descriptor = "Deceased"`, `cg_id = "Adamantinomatous Craniopharyngioma"`, `molecular_subtype = "CRANIO,
ADAM"`, `Kids_First_Participant_ID = "PT_WYXTEG3E"`, `match_id = "Deceased_PT_WYXTEG3E"`, `Variant_Classification =
"Frame_Shift_Del"`.
Caused by warning:
! 1 unknown level in `f`: Unavailable
ℹ Run ]8;;ide:run:dplyr::last_dplyr_warnings()dplyr::last_dplyr_warnings()]8;; to see the 8485 remaining warnings.
# Read color palette
palette_df <- readr::read_tsv(palette_file, guess_max = 100000, show_col_types = FALSE) %>%
mutate(color_names = factor(color_names),
color_names = fct_relevel(color_names, variants_order))
# Define and order palette
palette <- palette_df$hex_codes
names(palette) <- palette_df$color_names
# Define parameters for function
x_value <- PR_count_df$tumor_descriptor
title <- paste("Variant types in the paired longitudinal cohort", sep = " ")
# Run function
fname <- paste0(PR_plots_dir, "/", "Alteration_type_timepoints_barplots_PR.pdf")
print(fname)
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/Alteration_type_timepoints_barplots_PR.pdf"
p <- create_stacked_barplot_variant(df = PR_count_df, x = x_value, palette = palette, title = title)
pdf(file = fname, width = 6, height = 6)
print(p)
dev.off()
quartz_off_screen
2
# Define parameters for function
x_value <- PBTA_count_df$tumor_descriptor
title <- paste("Variant types in the PBTA cohort", sep = " ")
# Run function
fname <- paste0(PBTA_plots_dir, "/", "Alteration_type_timepoints_barplots_PBTA.pdf")
print(fname)
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/Alteration_type_timepoints_barplots_PBTA.pdf"
p <- create_stacked_barplot_variant(df = PBTA_count_df, x = x_value, palette = palette, title = title)
pdf(file = fname, width = 6, height = 6)
print(p)
dev.off()
quartz_off_screen
2
PR_panel_df <- PR_count_df %>%
mutate(cg_id = str_wrap(cg_id, 12)) # Edit to fit in the plot title for the panel
# Define parameters for function
x_value <- PR_panel_df$tumor_descriptor
title <- paste("Variant types across cancer groups in the paired longitudinal cohort", sep = " ")
rows <- 5
# Run function
fname <- paste0(PR_plots_dir, "/", "Alteration_type_timepoints_cg_id_barplots_PR.pdf")
print(fname)
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/Alteration_type_timepoints_cg_id_barplots_PR.pdf"
p <- create_stacked_barplot_variant_cg_id(df = PR_panel_df, x = x_value, palette = palette, title = title, rows = rows)
pdf(file = fname, width = 12, height = 15)
print(p)
dev.off()
quartz_off_screen
2
PBTA_panel_df <- PBTA_count_df %>%
mutate(cg_id = str_wrap(cg_id, 12)) # Edit to fit in the plot title for the panel
# Define parameters for function
x_value <- PBTA_panel_df$tumor_descriptor
title <- paste("Variant types across cancer groups in the PBTA cohort", sep = " ")
rows <- 10
# Run function
fname <- paste0(PBTA_plots_dir, "/", "Alteration_type_timepoints_cg_id_barplots_PBTA.pdf")
print(fname)
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/Alteration_type_timepoints_cg_id_barplots_PBTA.pdf"
p <- create_stacked_barplot_variant_cg_id(df = PBTA_panel_df, x = x_value, palette = palette, title = title, rows = rows)
pdf(file = fname, width = 15, height = 28)
print(p)
dev.off()
quartz_off_screen
2
PR_panel_df <- PR_count_df %>%
mutate(cg_id = str_replace_all(cg_id, " ", "_"),
molecular_subtype = str_wrap(molecular_subtype, 12)) # Edit to fit in the plot title for the panel
sample <- as.character(unique(PR_panel_df$cg_id))
sample <- sort(sample, decreasing = FALSE)
sample
[1] "Adamantinomatous_Craniopharyngioma" "Atypical_Teratoid_Rhabdoid_Tumor" "Chordoma"
[4] "Choroid_plexus_carcinoma" "CNS_Embryonal_tumor" "Craniopharyngioma"
[7] "Diffuse_midline_glioma" "Dysembryoplastic_neuroepithelial_tumor" "Embryonal_tumor_with_multilayer_rosettes"
[10] "Ependymoma" "Ewing_sarcoma" "Ganglioglioma"
[13] "Glial_neuronal_tumor" "Hemangioblastoma" "High_grade_glioma"
[16] "Low_grade_glioma" "Malignant_peripheral_nerve_sheath_tumor" "Medulloblastoma"
[19] "Meningioma" "Neuroblastoma" "Neurofibroma_Plexiform"
[22] "Pilocytic_astrocytoma" "Schwannoma"
# Loop through variable
for (i in seq_along(sample)){
print(i)
df_sub <- PR_panel_df %>%
filter(cg_id == sample[i])
if (i %in% c(10, 16)){
width_value = 25
}else{
width_value = 10
}
# Define parameters for function
x_value <- df_sub$tumor_descriptor
title <- paste(sample[i], "Variants across molecular subtypes", sep = ": ")
rows_value <- 1
# Run function
fname <- paste0(molecular_subtype_PR_plots_dir, "/", sample[i], "_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf")
print(fname)
p <- create_stacked_barplot_variant_molecular_subtype(df = df_sub, x = x_value, palette = palette, title = title, rows = rows_value)
pdf(file = fname, width = width_value, height = 6)
print(p)
dev.off()
}
[1] 1
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Adamantinomatous_Craniopharyngioma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 2
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Atypical_Teratoid_Rhabdoid_Tumor_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 3
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Chordoma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 4
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Choroid_plexus_carcinoma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 5
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/CNS_Embryonal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 6
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Craniopharyngioma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 7
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Diffuse_midline_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 8
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Dysembryoplastic_neuroepithelial_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 9
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Embryonal_tumor_with_multilayer_rosettes_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 10
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Ependymoma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 11
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Ewing_sarcoma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 12
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Ganglioglioma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 13
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Glial_neuronal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 14
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Hemangioblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 15
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/High_grade_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 16
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Low_grade_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 17
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Malignant_peripheral_nerve_sheath_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 18
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Medulloblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 19
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Meningioma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 20
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Neuroblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 21
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Neurofibroma_Plexiform_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 22
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Pilocytic_astrocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
[1] 23
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/molecular_subtype_PR_plots/Schwannoma_Alteration_type_timepoints_molecular_subtype_barplots_PR.pdf"
PBTA_panel_df <- PBTA_count_df %>%
mutate(cg_id = str_replace_all(cg_id, " ", "_"),
molecular_subtype = str_wrap(molecular_subtype, 12)) # Edit to fit in the plot title for the panel
sample <- as.character(unique(PBTA_panel_df$cg_id))
sample <- sort(sample, decreasing = FALSE)
sample
[1] "Adamantinomatous_Craniopharyngioma" "Astroblastoma"
[3] "Astrocytoma" "Atypical_choroid_plexus_papilloma"
[5] "Atypical_Teratoid_Rhabdoid_Tumor" "Cavernoma"
[7] "Central_neurocytoma" "Chondromyxoid_fibroma"
[9] "Chordoma" "Choroid_plexus_carcinoma"
[11] "Choroid_plexus_papilloma" "Choroid_plexus_tumor"
[13] "CNS_Burkitt's_lymphoma" "CNS_Embryonal_tumor"
[15] "CNS_neuroblastoma" "Craniopharyngioma"
[17] "Desmoplastic_infantile_astrocytoma_and_ganglioglioma" "Diffuse_fibrillary_astrocytoma"
[19] "Diffuse_hemispheric_glioma" "Diffuse_intrinsic_pontine_glioma"
[21] "Diffuse_leptomeningeal_glioneuronal_tumor" "Diffuse_midline_glioma"
[23] "Dysembryoplastic_neuroepithelial_tumor" "Embryonal_tumor_with_multilayer_rosettes"
[25] "Ependymoma" "Epstein_Barr_virus-related_tumor"
[27] "Ewing_sarcoma" "Extraventricular_neurocytoma"
[29] "Ganglioglioma" "Ganglioneuroblastoma"
[31] "Ganglioneuroma" "Germinoma"
[33] "Glial_neuronal_tumor" "Glioblastoma"
[35] "Hemangioblastoma" "High_grade_glioma"
[37] "Histiocytic_tumor" "Infant_type_hemispheric_glioma"
[39] "Inflammatory_Myofibroblastic_Tumor" "Langerhans_Cell_histiocytosis"
[41] "Low_grade_glioma" "Malignant_peripheral_nerve_sheath_tumor"
[43] "Medulloblastoma" "Melanocytic_tumor"
[45] "Meningioma" "Mesenchymal_tumor"
[47] "Metastatic_secondary_tumors" "Mixed_germ_cell_tumor"
[49] "Neuroblastoma" "Neurofibroma_Plexiform"
[51] "Non_germinomatous_germ_cell_tumor" "Oligodendroglioma"
[53] "Perineuroma" "Pilocytic_astrocytoma"
[55] "Pineoblastoma" "Pleomorphic_xanthoastrocytoma"
[57] "Rhabdomyosarcoma" "Rosai_Dorfman_disease"
[59] "Rosette_forming_glioneuronal_tumor" "Sarcoma"
[61] "Schwannoma" "Subependymal_Giant_Cell_Astrocytoma"
[63] "Teratoma"
# Loop through variable
for (i in seq_along(sample)){
print(i)
df_sub <- PBTA_panel_df %>%
filter(cg_id == sample[i])
if (i %in% c(25, 41)){
width_value = 25
}else{
width_value = 10
}
# Define parameters for function
x_value <- df_sub$tumor_descriptor
title <- paste(sample[i], "Variants across molecular subtypes", sep = ": ")
rows_value <- 1
# Run function
fname <- paste0(molecular_subtype_PBTA_plots_dir, "/", sample[i], "_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf")
print(fname)
p <- create_stacked_barplot_variant_molecular_subtype(df = df_sub, x = x_value, palette = palette, title = title, rows = rows_value)
pdf(file = fname, width = width_value, height = 6)
print(p)
dev.off()
}
[1] 1
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Adamantinomatous_Craniopharyngioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 2
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Astroblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 3
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Astrocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 4
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Atypical_choroid_plexus_papilloma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 5
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Atypical_Teratoid_Rhabdoid_Tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 6
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Cavernoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 7
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Central_neurocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 8
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Chondromyxoid_fibroma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 9
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Chordoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 10
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Choroid_plexus_carcinoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 11
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Choroid_plexus_papilloma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 12
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Choroid_plexus_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 13
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/CNS_Burkitt's_lymphoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 14
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/CNS_Embryonal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 15
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/CNS_neuroblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 16
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Craniopharyngioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 17
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Desmoplastic_infantile_astrocytoma_and_ganglioglioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 18
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Diffuse_fibrillary_astrocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 19
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Diffuse_hemispheric_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 20
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Diffuse_intrinsic_pontine_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 21
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Diffuse_leptomeningeal_glioneuronal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 22
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Diffuse_midline_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 23
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Dysembryoplastic_neuroepithelial_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 24
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Embryonal_tumor_with_multilayer_rosettes_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 25
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Ependymoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 26
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Epstein_Barr_virus-related_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 27
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Ewing_sarcoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 28
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Extraventricular_neurocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 29
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Ganglioglioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 30
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Ganglioneuroblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 31
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Ganglioneuroma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 32
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Germinoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 33
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Glial_neuronal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 34
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Glioblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 35
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Hemangioblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 36
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/High_grade_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 37
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Histiocytic_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 38
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Infant_type_hemispheric_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 39
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Inflammatory_Myofibroblastic_Tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 40
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Langerhans_Cell_histiocytosis_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 41
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Low_grade_glioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 42
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Malignant_peripheral_nerve_sheath_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 43
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Medulloblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 44
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Melanocytic_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 45
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Meningioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 46
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Mesenchymal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 47
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Metastatic_secondary_tumors_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 48
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Mixed_germ_cell_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 49
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Neuroblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 50
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Neurofibroma_Plexiform_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 51
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Non_germinomatous_germ_cell_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 52
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Oligodendroglioma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 53
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Perineuroma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 54
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Pilocytic_astrocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 55
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Pineoblastoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 56
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Pleomorphic_xanthoastrocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 57
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Rhabdomyosarcoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 58
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Rosai_Dorfman_disease_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 59
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Rosette_forming_glioneuronal_tumor_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 60
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Sarcoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 61
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Schwannoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 62
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Subependymal_Giant_Cell_Astrocytoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
[1] 63
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PBTA/molecular_subtype_PBTA_plots/Teratoma_Alteration_type_timepoints_molecular_subtype_barplots_PBTA.pdf"
cg_df <- PR_count_df %>%
# Fix syntax in cancer groups names
mutate(cg_id = str_replace_all(cg_id, " ", "_")) %>%
arrange(tumor_descriptor, desc(molecular_subtype))
sample <- as.character(unique(cg_df$cg_id))
sample <- sort(sample, decreasing = FALSE)
sample
[1] "Adamantinomatous_Craniopharyngioma" "Atypical_Teratoid_Rhabdoid_Tumor" "Chordoma"
[4] "Choroid_plexus_carcinoma" "CNS_Embryonal_tumor" "Craniopharyngioma"
[7] "Diffuse_midline_glioma" "Dysembryoplastic_neuroepithelial_tumor" "Embryonal_tumor_with_multilayer_rosettes"
[10] "Ependymoma" "Ewing_sarcoma" "Ganglioglioma"
[13] "Glial_neuronal_tumor" "Hemangioblastoma" "High_grade_glioma"
[16] "Low_grade_glioma" "Malignant_peripheral_nerve_sheath_tumor" "Medulloblastoma"
[19] "Meningioma" "Neuroblastoma" "Neurofibroma_Plexiform"
[22] "Pilocytic_astrocytoma" "Schwannoma"
# Loop through variable
for (i in seq_along(sample)){
print(i)
df_sub <- cg_df %>%
filter(cg_id == sample[i])
if (i %in% c(2, 7, 15, 18)){
width_value = 25
}else if (i %in% c(10, 16)){
width_value = 36
}else{
width_value = 10
}
# Define parameters for function
x_value <- df_sub$tumor_descriptor
title <- paste(sample[i], "Variants across samples", sep = ": ")
rows_value <- 1
# Run function
fname <- paste0(kids_molecular_subtype_PR_plots_dir, "/", sample[i], "_Alteration_type_timepoints_kids_barplots_PR.pdf")
print(fname)
p <- create_stacked_barplot_variant_kids(df = df_sub, x = x_value, palette = palette, title = title, rows = rows_value)
pdf(file = fname, width = width_value, height = 6)
print(p)
dev.off()
}
[1] 1
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Adamantinomatous_Craniopharyngioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 2
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Atypical_Teratoid_Rhabdoid_Tumor_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 3
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Chordoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 4
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Choroid_plexus_carcinoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 5
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/CNS_Embryonal_tumor_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 6
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Craniopharyngioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 7
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Diffuse_midline_glioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 8
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Dysembryoplastic_neuroepithelial_tumor_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 9
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Embryonal_tumor_with_multilayer_rosettes_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 10
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Ependymoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 11
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Ewing_sarcoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 12
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Ganglioglioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 13
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Glial_neuronal_tumor_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 14
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Hemangioblastoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 15
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/High_grade_glioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 16
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Low_grade_glioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 17
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Malignant_peripheral_nerve_sheath_tumor_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 18
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Medulloblastoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 19
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Meningioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 20
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Neuroblastoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 21
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Neurofibroma_Plexiform_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 22
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Pilocytic_astrocytoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 23
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_molecular_subtype_PR_plots/Schwannoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
cg_df <- PR_count_df %>%
# Fix syntax in cancer groups names
mutate(cg_id = str_replace_all(cg_id, " ", "_"))
sample <- as.character(unique(cg_df$cg_id))
sample <- sort(sample, decreasing = FALSE)
sample
[1] "Adamantinomatous_Craniopharyngioma" "Atypical_Teratoid_Rhabdoid_Tumor" "Chordoma"
[4] "Choroid_plexus_carcinoma" "CNS_Embryonal_tumor" "Craniopharyngioma"
[7] "Diffuse_midline_glioma" "Dysembryoplastic_neuroepithelial_tumor" "Embryonal_tumor_with_multilayer_rosettes"
[10] "Ependymoma" "Ewing_sarcoma" "Ganglioglioma"
[13] "Glial_neuronal_tumor" "Hemangioblastoma" "High_grade_glioma"
[16] "Low_grade_glioma" "Malignant_peripheral_nerve_sheath_tumor" "Medulloblastoma"
[19] "Meningioma" "Neuroblastoma" "Neurofibroma_Plexiform"
[22] "Pilocytic_astrocytoma" "Schwannoma"
# Loop through variable
for (i in seq_along(sample)){
print(i)
df_sub <- cg_df %>%
filter(cg_id == sample[i])
if (i %in% c(2, 7, 15, 18)){
width_value = 25
}else if (i %in% c(10, 16)){
width_value = 28
}else{
width_value = 10
}
# Define parameters for function
x_value <- df_sub$tumor_descriptor
title <- paste(sample[i], "Variants across samples", sep = ": ")
rows <- 1
# Run function
fname <- paste0(kids_PR_plots_dir, "/", sample[i], "_Alteration_type_timepoints_kids_barplots_PR.pdf")
print(fname)
p <- create_stacked_barplot_variant_kids(df = df_sub, x = x_value, palette = palette, title = title, rows = rows)
pdf(file = fname, width = width_value, height = 6)
print(p)
dev.off()
}
[1] 1
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Adamantinomatous_Craniopharyngioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 2
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Atypical_Teratoid_Rhabdoid_Tumor_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 3
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Chordoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 4
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Choroid_plexus_carcinoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 5
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/CNS_Embryonal_tumor_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 6
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Craniopharyngioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 7
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Diffuse_midline_glioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 8
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Dysembryoplastic_neuroepithelial_tumor_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 9
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Embryonal_tumor_with_multilayer_rosettes_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 10
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Ependymoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 11
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Ewing_sarcoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 12
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Ganglioglioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 13
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Glial_neuronal_tumor_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 14
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Hemangioblastoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 15
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/High_grade_glioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 16
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Low_grade_glioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 17
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Malignant_peripheral_nerve_sheath_tumor_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 18
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Medulloblastoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 19
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Meningioma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 20
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Neuroblastoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 21
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Neurofibroma_Plexiform_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 22
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Pilocytic_astrocytoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
[1] 23
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_barplots_PR/kids_PR_plots/Schwannoma_Alteration_type_timepoints_kids_barplots_PR.pdf"
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] igraph_1.5.1 packcircles_0.3.6 gridBase_0.4-7 reshape2_1.4.4
[5] gridExtra_2.3 clonevol_0.99.11 devtools_2.4.5 usethis_2.2.2
[9] CopyNumberPlots_1.18.0 karyoploteR_1.28.0 regioneR_1.34.0 BiocManager_1.30.22
[13] readxl_1.4.3 Matrix_1.6-2 future_1.33.0 scater_1.30.0
[17] scuttle_1.12.0 SeuratObject_5.0.0 Seurat_5.0.0 scDblFinder_1.16.0
[21] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0 Biobase_2.62.0 GenomicRanges_1.54.1
[25] GenomeInfoDb_1.38.1 IRanges_2.36.0 S4Vectors_0.40.1 BiocGenerics_0.48.1
[29] MatrixGenerics_1.14.0 matrixStats_1.1.0 ggthemes_4.2.4 ggpubr_0.6.0
[33] rstatix_0.7.2 flextable_0.9.4 reshape_0.8.9 ComplexHeatmap_2.18.0
[37] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.3
[41] purrr_1.0.2 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[45] ggplot2_3.4.4 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] dichromat_2.0-0.1 vroom_1.6.4 progress_1.2.2 urlchecker_1.0.1 nnet_7.3-19
[6] goftest_1.2-3 Biostrings_2.70.1 vctrs_0.6.4 spatstat.random_3.2-1 digest_0.6.33
[11] png_0.1-8 shape_1.4.6 ggrepel_0.9.4 deldir_1.0-9 httpcode_0.3.0
[16] parallelly_1.36.0 MASS_7.3-60 fontLiberation_0.1.0 httpuv_1.6.12 foreach_1.5.2
[21] withr_2.5.2 xfun_0.41 ellipsis_0.3.2 survival_3.5-7 memoise_2.0.1
[26] crul_1.4.0 ggbeeswarm_0.7.2 profvis_0.3.8 bamsignals_1.34.0 systemfonts_1.0.5
[31] ragg_1.2.6 zoo_1.8-12 GlobalOptions_0.1.2 pbapply_1.7-2 Formula_1.2-5
[36] prettyunits_1.2.0 KEGGREST_1.42.0 promises_1.2.1 httr_1.4.7 restfulr_0.0.15
[41] rhdf5filters_1.14.1 globals_0.16.2 fitdistrplus_1.1-11 ps_1.7.5 rhdf5_2.46.0
[46] rstudioapi_0.15.0 miniUI_0.1.1.1 generics_0.1.3 processx_3.8.2 base64enc_0.1-3
[51] curl_5.1.0 zlibbioc_1.48.0 ScaledMatrix_1.10.0 polyclip_1.10-6 GenomeInfoDbData_1.2.11
[56] SparseArray_1.2.2 desc_1.4.2 xtable_1.8-4 doParallel_1.0.17 evaluate_0.23
[61] S4Arrays_1.2.0 BiocFileCache_2.10.1 hms_1.1.3 irlba_2.3.5.1 colorspace_2.1-0
[66] filelock_1.0.2 ROCR_1.0-11 reticulate_1.34.0 spatstat.data_3.0-3 magrittr_2.0.3
[71] lmtest_0.9-40 later_1.3.1 viridis_0.6.4 lattice_0.22-5 spatstat.geom_3.2-7
[76] future.apply_1.11.0 scattermore_1.2 XML_3.99-0.15 cowplot_1.1.1 RcppAnnoy_0.0.21
[81] Hmisc_5.1-1 pillar_1.9.0 nlme_3.1-163 iterators_1.0.14 compiler_4.3.1
[86] beachmat_2.18.0 stringi_1.7.12 tensor_1.5 GenomicAlignments_1.38.0 plyr_1.8.9
[91] crayon_1.5.2 abind_1.4-5 BiocIO_1.12.0 locfit_1.5-9.8 sp_2.1-1
[96] bit_4.0.5 codetools_0.2-19 textshaping_0.3.7 BiocSingular_1.18.0 openssl_2.1.1
[101] bslib_0.5.1 biovizBase_1.50.0 GetoptLong_1.0.5 plotly_4.10.3 mime_0.12
[106] splines_4.3.1 circlize_0.4.15 Rcpp_1.0.11 dbplyr_2.4.0 sparseMatrixStats_1.14.0
[111] cellranger_1.1.0 knitr_1.45 blob_1.2.4 utf8_1.2.4 clue_0.3-65
[116] AnnotationFilter_1.26.0 fs_1.6.3 checkmate_2.3.0 listenv_0.9.0 DelayedMatrixStats_1.24.0
[121] pkgbuild_1.4.2 ggsignif_0.6.4 callr_3.7.3 statmod_1.5.0 tzdb_0.4.0
[126] pkgconfig_2.0.3 tools_4.3.1 cachem_1.0.8 RSQLite_2.3.3 viridisLite_0.4.2
[131] DBI_1.1.3 exomeCopy_1.48.0 fastmap_1.1.1 rmarkdown_2.25 scales_1.2.1
[136] ica_1.0-3 Rsamtools_2.18.0 broom_1.0.5 sass_0.4.7 officer_0.6.3
[141] patchwork_1.1.3 dotCall64_1.1-0 VariantAnnotation_1.48.0 carData_3.0-5 rpart_4.1.21
[146] RANN_2.6.1 farver_2.1.1 yaml_2.3.7 foreign_0.8-85 rtracklayer_1.62.0
[151] cli_3.6.1 leiden_0.4.3 lifecycle_1.0.4 askpass_1.2.0 uwot_0.1.16
[156] sessioninfo_1.2.2 bluster_1.12.0 backports_1.4.1 BiocParallel_1.36.0 timechange_0.2.0
[161] gtable_0.3.4 rjson_0.2.21 ggridges_0.5.4 progressr_0.14.0 parallel_4.3.1
[166] limma_3.58.1 jsonlite_1.8.7 edgeR_4.0.1 bitops_1.0-7 bit64_4.0.5
[171] xgboost_1.7.5.1 Rtsne_0.16 spatstat.utils_3.0-4 BiocNeighbors_1.20.0 zip_2.3.0
[176] bezier_1.1.2 jquerylib_0.1.4 metapod_1.10.0 dqrng_0.3.1 lazyeval_0.2.2
[181] shiny_1.7.5.1 htmltools_0.5.7 sctransform_0.4.1 rappdirs_0.3.3 ensembldb_2.26.0
[186] glue_1.6.2 gfonts_0.2.0 spam_2.10-0 XVector_0.42.0 gdtools_0.3.4
[191] RCurl_1.98-1.13 rprojroot_2.0.4 scran_1.30.0 BSgenome_1.70.1 cn.mops_1.48.0
[196] R6_2.5.1 labeling_0.4.3 GenomicFeatures_1.54.1 cluster_2.1.4 pkgload_1.3.3
[201] Rhdf5lib_1.24.0 ProtGenerics_1.34.0 DelayedArray_0.28.0 tidyselect_1.2.0 vipor_0.4.5
[206] htmlTable_2.4.2 xml2_1.3.5 fontBitstreamVera_0.1.1 car_3.1-2 AnnotationDbi_1.64.1
[211] rsvd_1.0.5 munsell_0.5.0 KernSmooth_2.23-22 fontquiver_0.2.1 data.table_1.14.8
[216] htmlwidgets_1.6.2 RColorBrewer_1.1-3 biomaRt_2.58.0 rlang_1.1.2 spatstat.sparse_3.0-3
[221] spatstat.explore_3.2-5 remotes_2.4.2.1 uuid_1.1-1 fansi_1.0.5 beeswarm_0.4.0